RESOLUTION IN THREE DIMENSIONS

Chromatography. Mobility. Mass. When mass resolution and chromatography are

not enough, high-efficiency T-Wave ion mobility gives you an additional dimension

of separation, based on molecular size and shape.

THE BENEFITS ARE CLEAR

www.waters.com/proof

PROTEOMICS BIOMARKERDISCOVERYPHARMACEUTICALS LIPIDOMICS

STRUCTURALELUCIDATION METABONOMICS BIOPHARMACEUTICALS

STRUCTURALBIOLOGYPOLYMERSPETROLEUMCHARACTERIZATION

IMAGING METABOLITEIDENTIFICATIONNANOPARTICLESFOODRESEARCH

SYNAPT delivers a third dimension of resolution to your analysis, proven to

transform your levels of insight and confidence whatever the application.

Chromatography. Mobility. Mass. When mass resolution and chromatography are

not enough, high-efficiency T-Wave ion mobility gives you an additional dimension

of separation, based on molecular size and shape.

PROTEOMICS BIOMARKERDISCOVERYPHARMACEUTICALS LIPIDOMICS

STRUCTURALELUCIDATION METABONOMICS BIOPHARMACEUTICALS

STRUCTURALBIOLOGYPOLYMERSPETROLEUMCHARACTERIZATION

IMAGING METABOLITEIDENTIFICATIONNANOPARTICLESFOODRESEARCH

YOU LEAD THE DISCOV ERY – W ITH OUR LEADING T ECHNOLOGY

Quadrupole

ZSpray™Source

Information. SYNAPT G2-Si uses high efficiency T-Wave ion mobility to significantly

enhance the peak capacity, specificity and sensitivity of your analysis.

Informatics. SYNAPT G2-Si combines T-Wave ion mobility with innovative software

to transform your targeted and untargeted workflows.

Impact. SYNAPT G2-Si provides a unique discovery advantage today,

and the greatest potential to meet your future needs.

If you need to be first to discover or first to publish, look no further than SYNAPT High Definition Mass Spectrometry.

The unique ability to use the collision cross section (CCS) property of an ion, through the use of T-Wave ion mobility,

delivers unique analytical benefits to a wide range of applications.

■■ The ultimate in qualitative and quantitative performance StepWave, QuanTof, and MSE ‘data

independent’ acquisition combine to

provide the most comprehensive and

confident untargeted identification and

quantification of compounds with

UPLC/MS/MS, at the lowest concentration

levels in complex matrices.

■■ Breakthrough SYNAPT High Definition MS™ Every scientist can extract unparalleled

information content and make new

discoveries not possible by any other

method, by combining high efficiency

T-wave ion mobility separations with

high resolution exact mass tandem MS.

■■ Maximum versatility

Serve the broadest range of applications

with the most extensive range of

targeted data acquisition methods,

chromatographic inlet, and ionization

source capabilities.

■■ Instant efficiency

Realize maximum system usability

and workflow efficiency across your

organization through Waters design

philosophy of Engineered Simplicity.™

■■ Accelerated success

Maximize your success with complete

system solutions backed by a superior

applications and technical support network.

QuanTof’s high-field

pusher and dual-stage

reflectron, incorporating

high-transmission parallel

wire grids, reduce ion

turnaround times due to

pre-push kinetic energy

spread and improve

focusing of high energy

ions respectively.

These innovative

technologies combine

to provide the highest

levels of Tof performance.

The unique ion detection

system combines an ultra-

fast electron multiplier

and ‘hybrid ADC’ detector

electronics to provide

outstanding sensitivity and

quantitative performance.

Dual-stage reflectron

Ion mirror Ion detection system

High field pusher

QuanTof Technology delivers an outstanding

combination of performance attributes:

■■ Over 50,000 FWHM mass resolving power

■■ Exact mass (<1 ppm RMS)

■■ Accurate isotope abundances

■■ In-spectrum dynamic range and linearity

in detector response of up to 106

■■ Up to 30 spectra/sec

■■ Maximum ToF duty cycle for HD-MRM

and HD-DDA methods

EX PERIENCE T HE ULT IMAT E IN QUALITAT IV E AND QUANT ITAT IV E PERFORMANCE

When your progress is limited by missing information or the risk of false positive results in your analysis, the

combination of StepWave ion optics, the QuanTof analyzer and MSE ‘data-independent’ acquisitions will maximize

your chances of success. By providing the best qualitative and quantitative performance attributes, these innovative

technologies significantly increase compound coverage and confidence in identification, characterization,

and quantitation for your most demanding applications.

First Stage

Second Stage

Focused Ion Beam

Eliminated neutrals

Conjoined T-Wave devices

Source

SYNAPT G2-Si is equipped with

a larger ion sampling orifice,

an enhanced vacuum pumping

configuration and revolutionary

StepWave ion transfer optics.

This groundbreaking dual-T-Wave,

off-axis design transfers ions from

the ion source to the quadrupole

MS analyzer with the highest

possible efficiency, at the same time

as ensuring undesirable neutral

contaminants are actively filtered out.

This dramatically increases MS

ion intensities while minimizing

background noise – significantly

improving detection limits and the

repeatability of quantitative assays.

■■ Selectivity and accuracy

QuanTof delivers high resolution, exact mass, accurate isotope

abundance, a wide dynamic range and speed of acquisition,

without compromise, for UPLC separation of very complex samples.

■■ Sensitivity and linearity

Stepwave and QuanTof provide LOD, LOQs at significantly lower

concentrations than ever thought possible with high resolution

MS, with exceptional linearity and reproducibility, even in the

most complex matrices.

■■ Maximum coverage

Eliminate the risk of incomplete analysis with UPLC®/MS,E

a simple patented method of data acquisition that

comprehensively catalogs samples in a single analysis.

■■ Simple, complete assays

Quantify with all the benefits of oa-Tof, MS,E Tof-MRM and HD-MRM:■■ Quantify and confirm unlimited numbers of components

in one analysis ■■ Eliminate or reduce time-consuming method development■■ Interrogate archived datasets to detect, identify,

and quantity new compounds

Ultra-high sensitivity

m/z684.200 684.300 684.400 684.500

%

0

100

1.18e4

684.35

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1�0�0� 3�4�16�8�4�.�3�5�

4�8�0�.�2�6�3�3�3�.�1�9�

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9�4�2�.�4�4� 1�2�8�5�.�5�5�

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8�1�3�.�3�9�

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StepWave source

Previous generation source

30X increase1

Data shows the relative increase in signal intensity for a fragment ion of [Glu1]-Fibrinopeptide B.

m/z955 956 957 958 959 960

%

0

100956.4304

956.2614

956.0925

955.9270

956.5959

956.7614

956.9304

957.0960

957.2616

>50,000

ResolutionFWHM

High mass resolution

Data shows the isotope distribution for the [M+6H]6+ species of Bovine Insulin.

In-spectrum dynamic range

m/z785 786 787

%

0

100

Intensity - 535 (1.20 ppm error)

785.8436

(1.10 ppm error)786.3449

(0.60 ppm error)786.8448

m/z600 800 1000 1200 1400 1600 1800

%

0

100

Intensity - 6.04 x 106

(3.00 ppm error) 956.4455

(3.30 ppm error) 1147.5332

(1.80 ppm error) 1434.1624

(0.85 ppm error) 819.9525

>4 orders per second

Data shown is for Bovine Insulin (left) and [Glu1]-Fibrinopeptide B (right) at > 10,000X magnification.

Accurate quantitation > 4 orders of linearity, with UPLC/MSE

m/z100 120 140 160 180 200 220 240 260 280 300 320 340 360

%

0

100311.0816

209.3962123.8988 179.3056 245.1001 280.3845 349.0429

m/z100 120 140 160 180 200 220 240 260 280 300 320 340 360

%

0

100 156.0776

127.0507

311.0808

245.1049

218.0229176.0325 287.1771 364.2942329.3606

-1.1mDa

-0.6mDa

-0.6mDa

+0.2mDa

Conc0.0 10.0 20.0 30.0 40.0 50.0

Res

ponse

0

5000

10000

15000

20000

25000

30000

35000

40000

45000

50000 ULOQ–500 pg on columnLLOQ–25 fg on column4.3 orders of linearityResiduals <20%R2 = 0.99

MS

MSE

10X improvementin LOQ versus previous generation source2

Simultaneous quantitation and identification with UPLC/MS.E Every component is recorded with molecular (MS) and fragment (MSE) ion spectra to aid compound identification. The mass spectral data shown is from 2.5 pg of Sulfadimethoxine on column.

TRAP T-Wave

IMS T-Wave

Drift Time

Inte

nsity

Why ion mobility?

Measuring the mobility, or drift time, of

an ion can yield information about its

structure, as compact ions with small

collision cross-sections drift quicker than

extended ions with large collision cross-

sections. Mixtures of compact and extended

ions can be separated in the gas phase.

IMS T-Wave

Drift Time

Inte

nsity

2 2.5 3.5 4.53 4 5Arrival Time (ms)

(GRGDS)2+

211.7 Å2 (SDGRG)2+

222.7 Å2

100

80

60

40

20

0

Rel

ativ

e In

tensi

ty (

%)

IM Resolution of over 40 (Ω/ΔΩ)3

The SYNAPT G2-Si System provides a unique platform to further

your discovery efforts by providing capabilities that go beyond

conventional MS instrumentation.

SYNAPT High Definition Mass Spectrometry® is the combination

of high-efficiency T-Wave ion mobility measurements and

separations with high-performance tandem MS, enabling the

differentiation of samples by size, shape and charge, as well as mass.

By introducing the orthogonal dimension of gas-phase ion

mobility separation, you can take advantage of a molecule’s

Collision Cross Section to significantly enhance separation,

specificity, sensitivity and structural insight in your analysis.

SYNAPT G2-Si High Definition MS with

Triwave Technology offers:

■■ Rapid, high-efficiency, T-Wave ion mobility separations

■■ Removal of interferences, purification of spectra

■■ Significant increases in analytical peak capacity

■■ Separation of isomers, conformers, and isobaric compounds

■■ Enhanced compound ID and structural characterization

■■ Simple, reproducible CCS measurements

■■ Comprehensive informatics tools to accelerate visualization,

processing, and interpretation of multidimensional

SYNAPT G2-Si HDMS™ data

Ever wondered what components you might be missing because high mass resolution or your current tandem MS methods don’t provide enough selectivity? Frustrated that your existing MS techniques can’t address certain challenges?

BREAK T HROUGH W IT H SYNAPT HIGH DEFINIT ION MS

Enhanced IM separation power – the high ion mobility resolving power of SYNAPT G2-Si enables a mixture of two reverse sequence peptides (GRGDS and SDGRG) differing in CCS (Ω) by only 5%3 to be easily separated. A mobility resolution in excess of 40 (Ω/ΔΩ) is indicated.

Ion Mobility Separation (IMS) T-Wave

TRANSFER T-Wave

For access to a unique range of

experimental possibilities to improve

identification, characterization or

localization of specific compounds,

Triwave is the key. Triwave employs

three T-Wave™ ion guides, allowing

ions to be trapped and accumulated,

separated based on their mobility,

and then transferred to the QuanTof

analyzer for high-resolution analysis.

Triwave’s innovative configuration

also ensures that the introduction

of IM is not made at the expense

of sensitivity.

High ion mobility resolution has been

achieved through increased operating

pressure in the Triwave device (via the

addition of a novel Helium filled entry

cell in the IMS T-Wave).3 The TRAP

and TRANSFER T-Wave regions can

be used independently or together

as collision cells, with (HDMS mode)

or without (TOF mode) ion mobility

separations, providing a unique

and diverse range of experimental

possibilities for improved and more

complete structural characterization.

T RANSFORM YOUR CAPACIT Y TO DISCOV ER

By combining high-efficiency ion mobility

separations with a high resolution time-of-

flight analyzer, SYNAPT G2-Si provides a

large increase in analytical peak capacity,

and delivers more information than is

available with the highest chromatographic

or mass resolution alone.

The orthogonal separation afforded

by high-efficiency IM separation

dramatically increases the number of

detectable and identifiable components

in complex mixtures by rapidly separating

molecules of the same mass-to-charge

ratio, while also providing measurements

related to their gas-phase conformation.

To provide unambiguous confirmation of

compound identity, the combination of

ion mobility and MSE ‘data independent’

acquisition (HDMSE) means fragment

ion information is attainable for every

detectable component and with

TransOmics,™ BiopharmaLynx,™ High

Definition Imaging, DynamX™ (HDX), and

UNIFI® CCS Research Edition (for small

molecules) you can now access all these

benefits quickly and easily across a wide

range of applications.

-9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 410n seconds

TOF MS IMS LC

A fully nested, parallel acquisition methodology

is the key to harnessing the full power of UPLC

(secs), high-efficiency IM separation (msecs), and

high resolution TOF MS (µsecs). The three separation

techniques provide seamless capability for separating

the most complex mixtures.

Uncovering unknown compounds fuels discovery and progress in scientific understanding. If you want to be able to see what others never have, the unique geometry of SYNAPT systems provide an unrivalled discovery advantage.6,9

PEAK CAPACITY ION MOBILITY SEPARATION HDMSE AND CCS WORKFLOWS

retention mobility peak capacitym/z

singly charged <5x total MS peak capacitymultiply charged <10x total MS peak capacity

UPLC T-Wave IMS QuanTof LC/HDMS

x x =

singly charged up to 5x total MS peak capacitymultiply charged up to 10x total MS peak capacity

Providing isomer separation, and purified higher quality spectra5

MSE and HDMSE provide a simple, generic method to enable

comprehensive profiling of the most complex datasets so you don’t

have to redesign experiments for different sample sets. High quality

molecular and fragment ion spectra are generated for every detectable

component using retention time and/or (ion mobility) drift time alignment.

The comprehensive nature of every dataset means that you can simply

re-interrogate your data, not re-analyze your sample.

The extra selectivity afforded by ion mobility separations provides more

identifications and overall coverage for the most complex mixtures. m/z

100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500

%

0

100

m/z100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500

%

0

100

m/z100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500

%

0

1002: TOF MS ES+

2.32e5314.1323

231.0580

203.0624136.0564116.0512 163.0672175.0677

217.0789

288.1519245.1097

274.0994246.1127 289.1544

332.1421

333.1444

354.1225

1: TOF MS ES+ 6.50e4314.1331

231.0592

232.0596288.1513

274.0989

315.1338332.1425

333.1440

1: TOF MS ES+ 2.98e4288.1526

245.1099

204.0704

189.0469175.0712231.0940

217.0787

246.1131 268.1457

332.1420

289.1537

314.1308

333.1425

334.1440

Without HDMS Components 1 and 2

With HDMS Component 1

With HDMS Component 2

Component 1 Component 2

With HDMS 12,000 peptides

Without HDMS 6,000 peptides

log amount [fmol]co

unt

0

20

40

60

80

100

120

-1 -0.8 -0.2 0.2 0.6 1 1.4 1.8 2.2 2.6

Ion Mobility Separation gives an increase in analytical peak capacity with UPLC/IMS/MS

Increased numbers of peptide identifications at the lower concentrations (indicated by the

blue box) are achieved with the introduction of T-Wave ion mobility separations. Data is from a

proteomics study using UPLC/HDMS.E 4

SAMPLES

KNOWLEDGE

Sample Prep

UPLC/MSE

UPLC/HDMSE

Data Processing

Reporting

Hypothesis 1Hypothesis 2Hypothesis 3

MAXIMIZE YOUR ANALYTICAL CAPABILIT Y

SYNAPT G2-Si provides a unique and extensive range of analytical capabilities, making it possible to target and characterize specific molecules or families of components in much greater detail and with more confidence than ever before.

The collision cross-section (CCS)7 is an important

distinguishing characteristic of an ion that is

related to its chemical structure and three-

dimensional conformation in the gas-phase.

A molecule’s conformation can be influenced

by a number of factors, such as the number and

location of charges. The measured CCS of an

ion can be used to help confirm its identity or

investigate its structure.

CCS can be determined from T-Wave ion

mobility separations simply and quickly, for a

wide range of analytes from small molecules,

lipids and peptides, to larger species such as

polymers and protein complexes.

■■ Separation of individual isomers,

conformers, and isobaric compounds

■■ Determine sites of biotransformation

■■ Study structure at physiological

concentrations

■■ Analysis of heterogeneous samples

■■ Wide mass range capability

■■ An additional ‘matrix-tolerant’

identification point

■■ Minimize false positive and negatives

in results

Collision cross section – because shape matters

Investigation and differentiation of the drug Ondansetron and metabolite structures using travelling wave ion mobility mass spectrometry (both MS and MS/MS data) and molecular modelling.7

OndansetronTheoretical 107.7 Å2

T-Wave 107.4 Å2

GR90315Theoretical 109.8 Å2

T-Wave 110.4 Å2

GR63418Theoretical 111.2 Å2

T-Wave 111.5 Å2

GR60661Theoretical 111.4 Å2

T-Wave 111.7 Å2

CCS increases confidence in screening for targets.

In the analysis of a small scale proficiency sample (containing 8 target compounds with known CCS), a CCS filter of 2% was used to eliminate a false positive (not matching the CCS of the 8 target compounds) and a false negative (with correct CCS, and mass error of 7.5 ppm) by allowing the mass error tolerance to be relaxed.

No CCS With CCS With CCS

m/z error (+/-) 5 ppm 5 ppm 10 ppm

rt error (+/-) 2.5% 2.5% 2.5%

CCS error (+/-) – 2% 2%

Correct IDs 7/8 7/8 8/8

False Negatives 1 1 0

False Positives 1 0 0

MSMS of Parent at 455.2910 m/z

RMS error = 2.2 mDa RMS error = 1.6 mDa

RMS error = 0.6 mDa

A

B

C C

UPLC/TAP analysis of Verapamil(455.29 )

First generation fragments formed in Trap and

subsequentlyseparated by IMS

INPUT – Parent

OUTPUT – Exact mass first and second

generation fragmentation spectra

Second generation fragments formed in

Transfer and associated to first generation parent

based on drift-time

m/z

m/z

Automated structural identification of Verapamil with high resolution and exact mass by TAP fragmentation. All data acquisition, processing and structural assignment is performed automatically using MassLynx, MSE data viewer, and MassFragment Software.

Confident structural characterization of components, from small

organic molecules to modified peptide species demands the best in

structural coverage and data quality. TAP fragmentation provides

a distinct advantage for building a complete structure, through

superior fragment ion coverage, sensitivity and accuracy compared

to traditional MSn or MS/MS techniques.

Multiple components of interest can be individually selected

for TAP fragmentation in a UPLC gradient and then subjected

to two stages of CID which provide extensive fragmentation

with high resolution and exact mass to aid unambiguous

structural elucidation.

Ion mobility separation plays a key enabling role, separating first

generation fragments and second generation fragments and then,

through ‘drift time’ values, aiding the automated association of

fragments within the MSE data viewer software.

Time Aligned Parallel (TAP) fragmentation – for more complete structural elucidation

UNPARALLELED V ERSATILITY FOR TARGET ED ANALYSIS

Electron Transfer Dissociation – for when CID isn’t enough

When analyzing post-translational modifications and top-down

sequencing are all important, Electron Transfer Dissociation (ETD)

complements collision induced dissociation (CID). Developed

specifically to maximize confidence, flexibility, and ease-of-use,

the optional ETD capability of SYNAPT G2-Si is a uniquely

powerful feature for sequencing of biomolecules.

Characterization of o-linked glycosylated peptide from Erythropoietin using LC/MS/MS with ETD. The ETD spectrum shown here exhibits fragment ions of the peptide ion enabling location of modification to be determined.

Supplemental activation is employed routinely to deliver high levels of ETD fragmentation for enhanced sequence coverage. The data shown here is for the phosphopeptide at m/z 688 from a digest of bovine ßeta-Casein. Mixed mode CID/ETD DDA analysis provides high quality sequence information on the basis of charge state.

■■ High performance – high resolution, Exact Mass data and high

reaction efficiency generate the highest quality sequence data

■■ Flexible – to utilize a range of high-efficiency reagents as well

as employ Ion Mobility Separations with ETD for advanced

fundamental studies

■■ Easy-to-use and maintain – easy, stable introduction and quick

replenishment of ETD reagent to the MS through the simplicity

of the ETD glow discharge source

www.waters.com/ETD

m/z200 400 600 800 1000 1200 1400 1600 1800

%

0

1001061.9

710.2

z'4440.2

c''3331.1z'1

159.0

292.0

229.1

383.2

z'5511.2

c''6612.2

557.5708.0

1061.4

916.3915.8

c''7727.3

c''8798.3

1053.9

1040.9

916.8

1032.4

1062.4

1062.9

c''111683.6

c''101612.5z'8

1396.5z'7

1325.51063.4

z'61254.4

1063.9z'8

1397.5

c''111684.6

1831.71685.61686.6

z'141977.8

1832.7

1833.71978.81979.8

Precursor at m/z 708 (3+)(EAISPPDAA(S)*AAPLR)PTM Glycosylation, O-linked

ETDNo IMS

IMS

CID Supplemental

Activation

IMS T-WAVE

TRANSFER T-WAVE

Triwave provides a very flexible analytical platform for ETD studies.

TRAP T-WAVE

m/z200 400 600 800 1000 1200 1400 1600 1800 2000

%

0

1001032.1

1031.7

1009.6

z'5616.5

z'4487.4

c''3460.3

z'3374.3

247.2

c''4589.4

488.4

c''6846.5

z'6731.5

732.5

802.5

c''7974.6

847.5

1032.6

2064.2

2063.2

1033.1

c''111447.8z'10

1217.8z'9

1089.7

1090.7 c''101332.8

1219.8

2047.2

1448.82018.2c''12

1576.91605.0 c''14

1818.1

2065.2

2066.2

2067.2

2087.2

Precursor at m/z 688 (3+)FQ(pS)*EEQQQTEDELQDKPTM Phosphorylation

High Sensitivity MS/MS Workflows

Increase in spectral quality comparing standard and high transmission modes. LC/MS/MS data for peptide VILAGEVTTPVTVR from a tryptic digest of Escherichia coli acquired at the same point in the chromatographic peak.

Illustrating the enhancements in selectivity (from MS/MS) and sensitivity (high transmission mode) using high resolution MRM compared to standard full scan MS mode. The lower LOD for MRM was 250fg testosterone on-column.12

Standard Transmission

HighTransmission

m/z200 400 600 800 1000 1200

%

0

100

m/z200 400 600 800 1000 1200

%

0

100

773.4

759.4136.1 571.3185.2

326.2

1058.6774.4

872.5 1023.5 1242.71129.6

1058.6

773.4

571.3

136.1

86.1

185.2 470.3326.2

258.1

672.4

583.3

673.4

872.5

774.4

775.4

922.41001.5

923.4

1129.6

1130.61242.7

1131.6

1137.5

1243.7

1244.7

MRM S+

FullScan MS S+ 1.25 pg on column

Time0.50 1.00 1.50 2.00 2.50 3.00 3.50 4.00 4.50

%

0

100

0.50 1.00 1.50 2.00 2.50 3.00 3.50 4.00 4.50

%

0

1001: TOF MS ES+

289.217 0.0200Da6.77e3

2.46

S/N:RMS=21.44

0.47 0.70

2.85

2.73

3.153.30 4.113.813.56 4.37

1: TOF MSMS ES+ 97.065 0.0200Da

380S/N:RMS=91.47

0.400.30 0.63 1.05 1.32 1.55 4.392.452.211.96 2.63 3.933.703.302.82 3.14 4.15 4.81

Targeted Discovery

High Definition Data Directed Analysis (HD-DDA) significantly

increases limits of detection, and the number of detectable

compounds in mixtures with enhancements in10,11:

■■ Sensitivity – up to 10x increase in MS/MS signal intensity,

using an ion mobility-enabled high transmission mode.

■■ Speed – faster, smarter decision making for optimized spectral

acquisition time and increased number of MS/MS switches.

Targeted Quantitation

The SYNAPT G2-Si MRM methods enable more sensitive and

selective targeted quantitation, with the benefits of high resolution

MS/MS, and ion mobility separations12,13:

■■ Tof-MRM mode – High transmission mode giving up to 10x

sensitivity increase for improved LLOD and LLOQ. Includes

RADAR technology for full scan data to assist method

development.

■■ HD-MRM mode – uses T-Wave ion mobility separations to

increase selectivity on precursors or fragments, or to acquire

all fragment ion data simultaneously with up to 10x sensitivity.13

Includes HD RADAR for more selective full scan data.

V ERSATILITY– BECAUSE YOUR CHALLENGES DEMAND IT

SYNAPT G2-Si MS and MALDI SYNAPT G2-Si MS are next-generation quadrupole orthogonal acceleration Time-of-flight systems, which can be upgraded on site to incorporate next generation HDMS functionality.

SYNAPT G2-Si HDMS Systems (HDMS Mode and Tof Mode) Access unique benefits of high-efficiency IMS and enhanced tandem MS to carry out conformational studies, reduce spectral complexity/background interferences, and retrieve more information from fragmentation studies.

SYNAPT G2-Si MS System (Tof Mode) Access new levels of Tof performance and productivity with application specific system solutions.

nanoFlow™ ESI

ESI – Electrospray Ionization

APCI – Atmospheric Pressure Chemical Ionization

ESCi ® – Dual ESI and APCi

APPI – Atmospheric Pressure Photo Ionization

APCI – Atmospheric Pressure Chemical Ionization

APGC – Atmospheric Pressure Gas Chromatography

MALDI – Matrix Assisted Laser Desorption Ionization

ASAP – Atmospheric Solids Analysis Probe

Also compatible with DESI (Prosalia), DART (IonSense), LDTD (Phytronix), LAESI (Protea Biosciences), and TriVersa NanoMate (Advion) sources.

System upgradability – Future proof your lab

Because you never know what challenges are around

the corner, more inlet choices will serve you better:

■■ The ACQUITY UltraPerformance LC® family

of products is proven to be the most powerful

and flexible chromatographic inlet for mass

spectrometry based analysis today, featuring

2D RP/RP, Hydrogen Deuterium Exchange (HDX),

Ultra Performance Convergence Chromatography

(UPC2®), Advance Polymer Chromatography

(APC) and ‘plug and play’ nanoTile™ Technology.

■■ Waters Universal Ion Source Architecture,

engineered to take maximum advantage of

UPLC® allows the widest range of ionization

techniques as well as the very latest

innovations in ionization technologies.

INSTANT EFFICIENCY AND ACCELERAT ED SUCCESS W ITH ENGINEERED SIMPLICITY

High performance is key to productivity, but why should you have to work any harder to take advantage? Central to the design of SYNAPT G2-Si is Engineered Simplicity. This means that while SYNAPT G2-Si is engineered to handle your most complex applications, it’s also engineered to add simplicity and automation throughout your entire workflow.

Simplicity starts with IntelliStart

Get up and running quickly and the discoveries come even faster! SYNAPT G2-Si features IntelliStart™ Technology,

an intuitive interface that automates routine tasks. This technology ensures that all levels of scientist can operate

the instrument quickly and confidently, to generate reproducible UPLC/MS data of the highest quality.

SIMPLE SETUP OF DIVERSE EXPERIMENTS

AUTOMATED MS RESOLUTION AND

CALIBRATION CHECKS

AUTOMATED LC/MSSYSTEM CHECK

AUTOMATED SYSTEMMONITORING

PREPAREIntelliStart ensures your system is ready to run for experts and beginners alike, whether you utilize MS, UPLC /MS or nanoUPLC /MS.

ANALYZEWaters’ Universal Ion Source Architecture, QuanTof, StepWave, Triwave, UPLC /HDMS,E HD-DDA, HD-MRM, and ETD technologies, will equip you with an entirely new level of quantitative and qualitative capability.

DECIDEGenerate reports, share results and archive information easily with Waters laboratory informatics. Make decisions faster and better than ever before.

INTERPRETProcess, visualize, compare, and interpret the most complex data automatically. Then turn it into meaningful information quickly with Informatics software that support both MS and High Definition MS™ workflows across applications.

Be Assured. Choose Waters Global Services

Waters Global Services helps customers optimize

laboratory operations by providing superior service,

support, upgrades, training, and Waters Quality Parts.®

For more information, go to www.waters.com/services.

WHY LEADING RESEARCHERS ARE LEADING WITH SYNAPT HIGH DEFINIT ION MASS SPECT ROMET RY

To reach beyond the boundaries of conventional mass spectrometry, you can access the extra dimension of high-efficiency ion mobility separation offered by SYNAPT G2-Si HDMS, across a wide range of applications. When leading researchers are saying the benefits of the SYNAPT Mass Spectrometry Systems are this good, can you risk being out of the game?

“ We didn’t expect the results to be as good as they are. If we had to synthesize just these three metabolites, it would probably have taken several months, whereas the ion mobility LC-MS experiment and modeling calculations is probably around a week’s worth of work.”

DRUG METABOLITE ID MADE EASYChemistry World, July 2010www.chemistryworld.org

Increasing efficiency in pharmaceutical research and discovery

Helping understand the role of structure in biopharmaceutical characterization

“ It is shown that IMMS reveals 2 to 3 gas-phase conformer populations for IgG2s. In contrast, a single gas-phase conformer is revealed using IMMS for both an IgG1 antibody and a Cys-232 Ser mutant IgG2, both of which are homogeneous with respect to disulfide bonding. This provides strong evidence that the observed IgG2 gas-phase conformers are related to disulfide bond heterogeneity. Additionally, IMMS analysis of redox enriched disulfide isoforms allows unambiguous assignment of the mobility peaks to known disulfide structures. These data clearly illustrate how IMMS can be used to quickly provide information on the higher order structure of antibody therapeutics.”

BAGAL D., ET AL.Rapid Commun. Mass Spectrom. 2008; 22: 2898-2904.

Enhancing qualitative and quantitative proteomic analysis

“ The Waters SYNAPT G2 with ion mobility has greatly enhanced selectivity for proteomic analysis. An orthogonal measure, ion mobility dramatically improves the label-free MSE methodology used in our research. Relative to earlier technology, the new G2 HDMSE platform enables detailed fragment ion determination with well characterized chromatographic measures, producing more accurate peptide sequence determination with precise, reproducible quantification.”

ANDREW K. OTTENS, Ph.D.Assistant Professor of Anatomy & Neurobiology and Biochemistry,Virginia Commonwealth University, VA, USA

“ CCS measurements have the potential to transform the way people screen for known compounds, because unlike parameters like retention time, CCS values are unaffected by different matrices and chromatographic methods, and give you a much higher level of confidence that you found what you’re looking for.”

SEVERINE GOSCINNY Scientist WIV-ISP, Belgium

Improved confidence in challenging screening applications

WHY LEADING RESEARCHERS ARE LEADING WITH SYNAPT HIGH DEFINIT ION MASS SPECT ROMET RY

Enhanced spatial localization in tissues: High Definition Imaging (HDI) MALDI

To determine the efficacy of a drug, it is critical

to understand how it’s distributed within

plant or animal tissue. Imaging by MALDI MS

provides this capability. Whether you want

to determine the location of peptides, lipids,

drugs, or drug metabolites, HDI™ MALDI – the

combination of high-efficiency ion mobility

separations and MALDI – uniquely offers the

ability to determine the distribution of your

target compound without interference from

simultaneously ionized background ions.

“ …imaging IM-MS provides several unique advantages including (1) selective imaging of isobaric species (i.e. lipids versus peptides) or structural/conformational subpopulations of the same species on the basis of IM, (2) separation/rejection of undesirable endogenous chemical noise, (3) reduction of ion suppression effects in the source of the Tof-MS, by temporal IM separation of analytes, and (4) potential utility for nearly simultaneous IM-MS/MS of all analytes at a particular pixel coordinate.”

MCLEAN J. A., RIDENOUR W. B., CAPRIOLI R. M.J Mass Spectrom. 2007 Aug; 42(8):1099-105.

“ IMS/MS is starting to attract devotees among analytical scientists who recognize the decisive benefits that come from coupling mass analysis with shape-dependent ion separation. As Prof. [Jim] Scrivens [from the University of Warwick, UK] put it, ‘The ability to track families of ions is one extraordinarily powerful aspect of this technique.’ More generally, he added, IMS/MS offers a platform ‘for separating and visualizing all of these different types of compounds in one high-information-content experiment that is superior to other approaches.’ ”

DOUBLING UP ON MASS ANALYSIS Chemical & Engineering News. March 29, 2010 Volume 88, Number 13 pp. 35-37.

Expanding scientists ability to better characterize polymer microstructure

Helping understand the role of structure in biopharmaceutical characterization

Structural Biology: Unique insights into biological mechanisms

Providing a totally new dimension,

SYNAPT is the MS platform of choice

for the rapid structural analysis of large

heterogeneous protein complexes.

Dozens of papers have been published

based on the unique abilities of

SYNAPT High Definition MS.1

Enhancing structural characterization of proteins with HDX and ion mobility“Importantly, ion mobility separations provided an orthogonal dimension of separation in addition to the reversed-phase high-performance liquid chromatography (RP-HPLC). The additional dimension of separation allowed for the deconvolution of overlapping isotopic patterns for co-eluting peptides and extraction of valuable deuterium incorporation data for those peptides. Taken together, these results indicate that including ion mobility separation in HX MS analyses further improves the mass spectrometry portion of such experiments.”

IACOB R. E., ET AL. Rapid Commun. Mass Spectrom. 2008; 22: 2898–2904.

>1.8 Million Effective Resolution

Visualization of the distributions of two ions (shown in red in the m/z versus drift time plot) which differ significantly in drift time but have a mass difference so small that it would require a m/z resolving power in excess of 1.8 million to achieve differentiation of the ions without T-Wave IMS separation.

The spatial distributions of the two ions are clearly different, when plotted using m/z and drift time to generate the images, as shown in the two panels for m/z 545.9499 and m/z 545.9502.

The MALDI SYNAPT G2-Si uses a 2.5KHz solid state laser and enables imaging to be performed down to 15 µm spatial resolution.

References (or Footnotes) – Header 2 in white

1. Author, X.X., et al. Title. Publication References - Italic. 261 (2007) 1-12.

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Waters, T he Science of What’s Possible, SYNAPT, High Definition Mass Spectrometry, High Definition MS, UPLC, ACQUITY UltraPerformance LC, TRIZAIC UPLC, Waters Quality Parts, UPC,2 and Triwave are registered trademarks of Waters Corporation. HDMS, IntelliStart, StepWave, Engineered Simplicity, nanoTile, ProteinLynx, BiopharmaLynx, TransOmics, HDI, T-Wave, DynamX, ZSpray, and DriftScope are trademarks of Waters Corporation. All other trademarks are the property of their respective owners.

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References

1. Dramatically Enhanced Analytical Sensitivity with the Use of Novel StepWave Ion Transfer Technology in the SYNAPT G2-S System. Waters Technical Brief (720003964EN) at www.waters.com

2. A Step Change in High-Resolution Quantitative Performance Combining Novel StepWave, QuanTof, and MSE Technology in the SYNAPT G2-S System. Waters Technical Brief (720003963EN) at www.waters.com

3. Giles K., et al. Enhancements in Travelling Wave Ion Mobility Resolution. Rapid Commun. Mass Spectrom. 2011, 25, 1559-1566.

4. Rodriguez-Suarez, E., et al. An Ion Mobility Assisted Data Independent LC-MS Strategy for the Analysis of Complex Biological Samples. Current Anal. Chem. 2013, 9, 199-211. DOI: http://dx.doi.org/10.2174/157341113805218947

5. Advantages of Size/Shape Ion Mobility Separation for Metabolite ID: Collecting Cleaner and More Specific Data then Using HRMS Alone. Waters Technical Brief (720004741EN) at www.waters.com

6. Pringle, S. D., et al. An Investigation of the Mobility Separation of Some Peptide and Protein Ions Using a New Hybrid Quadrupole/Traveling Wave IMS/oa-TOF Instrument. Int. J. Mass Spectrom. 261 (2007) 1-12.

7. Dear G. J., et al. Sites of Metabolic Substitution: Investigating Metabolite Structures Utilizing Ion Mobility and Molecular Modelling. Rapid Commun. Mass Spectrom. 2010; 24: 3157-3162.

8. The Benefits of Gas-Phase Collision Cross-Section (CCS) Measurements in High-Resolution, Accurate-Mass UPLC/MS Analyses. Waters White Paper (720004749EN) at www.waters.com

9. Triwave White Paper (720004176EN) at www.waters.com

10. High Definition Data Directed Analysis (HD-DDA). Waters Technical Brief (720004734EN) at www.waters.com

11. High Definition Data Directed Analysis: The Application of Quadrupole Ion Mobility Time-of-Flight Mass Spectrometry for Untargeted Proteomics Studies. Waters Application Note (720004729EN) at www.waters.com

12. Targeted High Resolution Quantification with Tof-MRM and HD-MRM. Waters Technical Brief (720004728EN) at www.waters.com

13. High Definition Multiple Reaction Monitoring: The Application of Quadrupole Ion Mobility Time-of-Flight Mass Spectrometry for Targeted Proteomics Studies. Waters Application Note (720004730EN) at www.waters.com

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